gatk3的最后一个经典版本3.8

Chris Hartl 41a030f4b7 Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again: ... Part 1 of Variant Annotator Unit tests: PerReadAlleleLikelihoodMap - Added contract enforcement for public methods - Refactored the conversion from read -> (allele -> likelihood) to allele -> list[read] into its own method - added method documentation for non getters/setters - finals, finals everywhere - Add in a unit test for the PerReadAlleleLikelihoodMap. Complete coverage except for .clear() and a method that is a straight call into a separately-tested utility class.		2013-02-04 14:16:28 -05:00
licensing	Refrain from pushing symlinks into the repo... not all filesystems treat it correctly	2013-01-22 15:18:19 -07:00
protected/java	Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again:	2013-02-04 14:16:28 -05:00
public	Part 1 of Variant Annotator Unit tests: PerReadAlleleLikelihoodMap	2013-02-04 14:16:06 -05:00
settings	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Move AWS keys to a resources subdirectory within the phonehome package	2013-01-31 11:56:34 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00